This paper reports on the detection of gene mutation in circulating tumor cells (CTC) captured using the Ephesia microdevice. In an earlier work, we have demonstrated the advantages of the Ephesia system to capture rare CTCs in blood samples obtained from metastatic cancer patients . The device combines the advantages of both microfluidics and immunocapture to achieve high purity (below 0.01% contamination) and high capture efficiency (> 90% of EpCAM-positive cells). After an initial proof of concept using cells lines, the Ephesia system has recently been compared to the Veridex Cellsearch and validated with real patient samples. In this work, we show the possibility to release the captured cells and to perform a subsequent genomic analysis. The microchip design and analysis workflow was optimized to provide a capture purity which is compatible with conventional PCR.